1
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Kesapragada M, Sun YH, Zlobina K, Recendez C, Fregoso D, Yang HY, Aslankoohi E, Isseroff R, Rolandi M, Zhao M, Gomez M. Deep learning classification for macrophage subtypes through cell migratory pattern analysis. Front Cell Dev Biol 2024; 12:1259037. [PMID: 38385029 PMCID: PMC10879298 DOI: 10.3389/fcell.2024.1259037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Macrophages can exhibit pro-inflammatory or pro-reparatory functions, contingent upon their specific activation state. This dynamic behavior empowers macrophages to engage in immune reactions and contribute to tissue homeostasis. Understanding the intricate interplay between macrophage motility and activation status provides valuable insights into the complex mechanisms that govern their diverse functions. In a recent study, we developed a classification method based on morphology, which demonstrated that movement characteristics, including speed and displacement, can serve as distinguishing factors for macrophage subtypes. In this study, we develop a deep learning model to explore the potential of classifying macrophage subtypes based solely on raw trajectory patterns. The classification model relies on the time series of x-y coordinates, as well as the distance traveled and net displacement. We begin by investigating the migratory patterns of macrophages to gain a deeper understanding of their behavior. Although this analysis does not directly inform the deep learning model, it serves to highlight the intricate and distinct dynamics exhibited by different macrophage subtypes, which cannot be easily captured by a finite set of motility metrics. Our study uses cell trajectories to classify three macrophage subtypes: M0, M1, and M2. This advancement holds promising implications for the future, as it suggests the possibility of identifying macrophage subtypes without relying on shape analysis. Consequently, it could potentially eliminate the necessity for high-quality imaging techniques and provide more robust methods for analyzing inherently blurry images.
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Affiliation(s)
- Manasa Kesapragada
- Department of Applied Mathematics, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Yao-Hui Sun
- Department of Ophthalmology and Vision Science, School of Medicine, University of California, Davis, Sacramento, CA, United States
| | - Ksenia Zlobina
- Department of Applied Mathematics, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Cynthia Recendez
- Department of Ophthalmology and Vision Science, School of Medicine, University of California, Davis, Sacramento, CA, United States
| | - Daniel Fregoso
- Department of Dermatology, School of Medicine, UC Davis, Sacramento, CA, United States
| | - Hsin-Ya Yang
- Department of Dermatology, School of Medicine, UC Davis, Sacramento, CA, United States
| | - Elham Aslankoohi
- Department of Electrical and Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Rivkah Isseroff
- Department of Dermatology, School of Medicine, UC Davis, Sacramento, CA, United States
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Min Zhao
- Department of Ophthalmology and Vision Science, School of Medicine, University of California, Davis, Sacramento, CA, United States
- Department of Dermatology, School of Medicine, UC Davis, Sacramento, CA, United States
| | - Marcella Gomez
- Department of Applied Mathematics, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
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2
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Park Y, Hernandez S, Hernandez CO, Schweiger HE, Li H, Voitiuk K, Dechiraju H, Hawthorne N, Muzzy EM, Selberg JA, Sullivan FN, Urcuyo R, Salama SR, Aslankoohi E, Knight HJ, Teodorescu M, Mostajo-Radji MA, Rolandi M. Modulation of neuronal activity in cortical organoids with bioelectronic delivery of ions and neurotransmitters. Cell Rep Methods 2024; 4:100686. [PMID: 38218190 PMCID: PMC10831944 DOI: 10.1016/j.crmeth.2023.100686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/01/2023] [Accepted: 12/14/2023] [Indexed: 01/15/2024]
Abstract
Precise modulation of brain activity is fundamental for the proper establishment and maturation of the cerebral cortex. To this end, cortical organoids are promising tools to study circuit formation and the underpinnings of neurodevelopmental disease. However, the ability to manipulate neuronal activity with high temporal resolution in brain organoids remains limited. To overcome this challenge, we introduce a bioelectronic approach to control cortical organoid activity with the selective delivery of ions and neurotransmitters. Using this approach, we sequentially increased and decreased neuronal activity in brain organoids with the bioelectronic delivery of potassium ions (K+) and γ-aminobutyric acid (GABA), respectively, while simultaneously monitoring network activity. This works highlights bioelectronic ion pumps as tools for high-resolution temporal control of brain organoid activity toward precise pharmacological studies that can improve our understanding of neuronal function.
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Affiliation(s)
- Yunjeong Park
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sebastian Hernandez
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Centro de Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José 11501 2060, Costa Rica
| | - Cristian O Hernandez
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hunter E Schweiger
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Houpu Li
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kateryna Voitiuk
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Harika Dechiraju
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nico Hawthorne
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Elana M Muzzy
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - John A Selberg
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Frederika N Sullivan
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Roberto Urcuyo
- Centro de Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José 11501 2060, Costa Rica
| | - Sofie R Salama
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Institute for the Biology of Stem Cells, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Elham Aslankoohi
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Heather J Knight
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Institute for the Biology of Stem Cells, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
| | - Mohammed A Mostajo-Radji
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Institute for the Biology of Stem Cells, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Institute for the Biology of Stem Cells, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
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3
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Mehta AS, Teymoori S, Recendez C, Fregoso D, Gallegos A, Yang HY, Aslankoohi E, Rolandi M, Isseroff RR, Zhao M, Gomez M. Quantifying innervation facilitated by deep learning in wound healing. Sci Rep 2023; 13:16885. [PMID: 37803028 PMCID: PMC10558471 DOI: 10.1038/s41598-023-42743-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/14/2023] [Indexed: 10/08/2023] Open
Abstract
The peripheral nerves (PNs) innervate the dermis and epidermis, and are suggested to play an important role in wound healing. Several methods to quantify skin innervation during wound healing have been reported. Those usually require multiple observers, are complex and labor-intensive, and the noise/background associated with the immunohistochemistry (IHC) images could cause quantification errors/user bias. In this study, we employed the state-of-the-art deep neural network, Denoising Convolutional Neural Network (DnCNN), to perform pre-processing and effectively reduce the noise in the IHC images. Additionally, we utilized an automated image analysis tool, assisted by Matlab, to accurately determine the extent of skin innervation during various stages of wound healing. The 8 mm wound is generated using a circular biopsy punch in the wild-type mouse. Skin samples were collected on days 3, 7, 10 and 15, and sections from paraffin-embedded tissues were stained against pan-neuronal marker- protein-gene-product 9.5 (PGP 9.5) antibody. On day 3 and day 7, negligible nerve fibers were present throughout the wound with few only on the lateral boundaries of the wound. On day 10, a slight increase in nerve fiber density appeared, which significantly increased on day 15. Importantly, we found a positive correlation (R2 = 0.926) between nerve fiber density and re-epithelization, suggesting an association between re-innervation and re-epithelization. These results established a quantitative time course of re-innervation in wound healing, and the automated image analysis method offers a novel and useful tool to facilitate the quantification of innervation in the skin and other tissues.
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Affiliation(s)
- Abijeet Singh Mehta
- Department of Dermatology, University of California, Davis, CA, 95616, USA.
- Department of Ophthalmology, University of California, Davis, CA, 95616, USA.
| | - Sam Teymoori
- Department of Applied Mathematics, University of California, Santa Cruz, CA, 95064, USA
| | - Cynthia Recendez
- Department of Dermatology, University of California, Davis, CA, 95616, USA
- Department of Ophthalmology, University of California, Davis, CA, 95616, USA
| | - Daniel Fregoso
- Department of Dermatology, University of California, Davis, CA, 95616, USA
| | - Anthony Gallegos
- Department of Dermatology, University of California, Davis, CA, 95616, USA
| | - Hsin-Ya Yang
- Department of Dermatology, University of California, Davis, CA, 95616, USA
| | - Elham Aslankoohi
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, CA, 95064, USA
| | | | - Min Zhao
- Department of Dermatology, University of California, Davis, CA, 95616, USA.
- Department of Ophthalmology, University of California, Davis, CA, 95616, USA.
| | - Marcella Gomez
- Department of Applied Mathematics, University of California, Santa Cruz, CA, 95064, USA.
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4
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Baniya P, Tebyani M, Asefifeyzabadi N, Nguyen T, Hernandez C, Zhu K, Li H, Selberg J, Hsieh HC, Pansodtee P, Yang HY, Recendez C, Keller G, Hee WS, Aslankoohi E, Isseroff RR, Zhao M, Gomez M, Rolandi M, Teodorescu M. A system for bioelectronic delivery of treatment directed toward wound healing. Sci Rep 2023; 13:14766. [PMID: 37679425 PMCID: PMC10485133 DOI: 10.1038/s41598-023-41572-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
The development of wearable bioelectronic systems is a promising approach for optimal delivery of therapeutic treatments. These systems can provide continuous delivery of ions, charged biomolecules, and an electric field for various medical applications. However, rapid prototyping of wearable bioelectronic systems for controlled delivery of specific treatments with a scalable fabrication process is challenging. We present a wearable bioelectronic system comprised of a polydimethylsiloxane (PDMS) device cast in customizable 3D printed molds and a printed circuit board (PCB), which employs commercially available engineering components and tools throughout design and fabrication. The system, featuring solution-filled reservoirs, embedded electrodes, and hydrogel-filled capillary tubing, is assembled modularly. The PDMS and PCB both contain matching through-holes designed to hold metallic contact posts coated with silver epoxy, allowing for mechanical and electrical integration. This assembly scheme allows us to interchange subsystem components, such as various PCB designs and reservoir solutions. We present three PCB designs: a wired version and two battery-powered versions with and without onboard memory. The wired design uses an external voltage controller for device actuation. The battery-powered PCB design uses a microcontroller unit to enable pre-programmed applied voltages and deep sleep mode to prolong battery run time. Finally, the battery-powered PCB with onboard memory is developed to record delivered currents, which enables us to verify treatment dose delivered. To demonstrate the functionality of the platform, the devices are used to deliver H[Formula: see text] in vivo using mouse models and fluoxetine ex vivo using a simulated wound environment. Immunohistochemistry staining shows an improvement of 35.86% in the M1/M2 ratio of H[Formula: see text]-treated wounds compared with control wounds, indicating the potential of the platform to improve wound healing.
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Affiliation(s)
- Prabhat Baniya
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
| | - Maryam Tebyani
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Narges Asefifeyzabadi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Tiffany Nguyen
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Cristian Hernandez
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Kan Zhu
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, CA, 95816, USA
- Department of Ophthalmology and Vision Science, University of California Davis, Sacramento, CA, 95817, USA
| | - Houpu Li
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - John Selberg
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Hao-Chieh Hsieh
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Pattawong Pansodtee
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Hsin-Ya Yang
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, CA, 95816, USA
| | - Cynthia Recendez
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, CA, 95816, USA
- Department of Ophthalmology and Vision Science, University of California Davis, Sacramento, CA, 95817, USA
| | - Gordon Keller
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Wan Shen Hee
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Elham Aslankoohi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Roslyn Rivkah Isseroff
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, CA, 95816, USA
| | - Min Zhao
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, CA, 95816, USA
- Department of Ophthalmology and Vision Science, University of California Davis, Sacramento, CA, 95817, USA
| | - Marcella Gomez
- Department of Applied Mathematics, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
| | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
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5
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Mehta AS, Teymoori S, Recendez C, Fregoso D, Gallegos A, Yang HY, Isseroff R, Zhao M, Gomez M, Aslankoohi E, Rolandi M. Quantifying innervation facilitated by deep learning in wound healing. Res Sq 2023:rs.3.rs-3088471. [PMID: 37461461 PMCID: PMC10350234 DOI: 10.21203/rs.3.rs-3088471/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The peripheral nerves (PNs) innervate the dermis and epidermis, which have been suggested to play an important role in wound healing. Several methods to quantify skin innervation during wound healing have been reported. Those usually require multiple observers, are complex and labor-intensive, and noise/background associated with the Immunohistochemistry (IHC) images could cause quantification errors/user bias. In this study, we employed the state-of-the-art deep neural network, DnCNN, to perform pre-processing and effectively reduce the noise in the IHC images. Additionally, we utilized an automated image analysis tool, assisted by Matlab, to accurately determine the extent of skin innervation during various stages of wound healing. The 8mm wound is generated using a circular biopsy punch in the wild-type mouse. Skin samples were collected on days 3,7,10 and 15, and sections from paraffin-embedded tissues were stained against pan-neuronal marker- protein-gene-product 9.5 (PGP 9.5) antibody. On day 3 and day 7, negligible nerve fibers were present throughout the wound with few only on the lateral boundaries of the wound. On day 10, a slight increase in nerve fiber density appeared, which significantly increased on day 15. Importantly we found a positive correlation (R 2 = 0.933) between nerve fiber density and re-epithelization, suggesting an association between re-innervation and re-epithelization. These results established a quantitative time course of re-innervation in wound healing, and the automated image analysis method offers a novel and useful tool to facilitate the quantification of innervation in the skin and other tissues.
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6
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Park Y, Hernandez S, Hernandez CO, Schweiger HE, Li H, Voitiuk K, Dechiraju H, Hawthorne N, Muzzy EM, Selberg JA, Sullivan FN, Urcuyo R, Salama SR, Aslankoohi E, Teodorescu M, Mostajo-Radji MA, Rolandi M. Modulation of neuronal activity in cortical organoids with bioelectronic delivery of ions and neurotransmitters. bioRxiv 2023:2023.06.10.544416. [PMID: 37333351 PMCID: PMC10274913 DOI: 10.1101/2023.06.10.544416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Precise modulation of brain activity is fundamental for the proper establishment and maturation of the cerebral cortex. To this end, cortical organoids are promising tools to study circuit formation and the underpinnings of neurodevelopmental disease. However, the ability to manipulate neuronal activity with high temporal resolution in brain organoids remains limited. To overcome this challenge, we introduce a bioelectronic approach to control cortical organoid activity with the selective delivery of ions and neurotransmitters. Using this approach, we sequentially increased and decreased neuronal activity in brain organoids with the bioelectronic delivery of potassium ions (K+) and γ-aminobutyric acid (GABA), respectively, while simultaneously monitoring network activity. This works highlights bioelectronic ion pumps as tools for high-resolution temporal control of brain organoid activity toward precise pharmacological studies that can improve our understanding of neuronal function.
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Affiliation(s)
- Yunjeong Park
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sebastian Hernandez
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Centro de Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, 11501 2060, Costa Rica
| | - Cristian O. Hernandez
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hunter E. Schweiger
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Houpu Li
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kateryna Voitiuk
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Harika Dechiraju
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nico Hawthorne
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Elana M. Muzzy
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John A. Selberg
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Roberto Urcuyo
- Centro de Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, 11501 2060, Costa Rica
| | - Sofie R. Salama
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Elham Aslankoohi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Mohammed A. Mostajo-Radji
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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7
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Hernandez C, Aslankoohi E, Frolikov P, Li H, Kurniawan S, Rolandi M. Implementing QR codes in academia to improve sample tracking, data accessibility, and traceability in multicampus interdisciplinary collaborations. PLoS One 2023; 18:e0282783. [PMID: 37023011 PMCID: PMC10079063 DOI: 10.1371/journal.pone.0282783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/22/2023] [Indexed: 04/07/2023] Open
Abstract
The growing number of multicampus interdisciplinary projects in academic institutions expedites a necessity for tracking systems that provide instantly accessible data associated with devices, samples, and experimental results to all collaborators involved. This need has become particularly salient with the COVID pandemic when consequent travel restrictions have hampered in person meetings and laboratory visits. Minimizing post-pandemic travel can also help reduce carbon footprint of research activities. Here we developed a Quick Response (QR) code tracking system that integrates project management tools for seamless communication and tracking of materials and devices between multicampus collaborators: one school of medicine, two engineering laboratories, three manufacturing cleanroom sites, and three research laboratories. Here we aimed to use this system to track the design, fabrication, and quality control of bioelectronic devices, in vitro experimental results, and in vivo testing. Incorporating the tracking system into our project helped our multicampus teams accomplish milestones on a tight timeline via improved data traceability, manufacturing efficiency, and shared experimental results. This tracking system is particularly useful to track device issues and ensure engineering device consistency when working with expensive biological samples in vitro and animals in vivo to reduce waste of biological and animal resources associated with device failure.
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Affiliation(s)
- Cristian Hernandez
- Department of Electrical and Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Elham Aslankoohi
- Department of Electrical and Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Pavel Frolikov
- Department of Computational Media, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Houpu Li
- Department of Electrical and Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Sri Kurniawan
- Department of Computational Media, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
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8
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Fonseca JP, Aslankoohi E, Ng AH, Chevalier M. Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling. PLoS Comput Biol 2022; 18:e1009873. [PMID: 35353814 PMCID: PMC9000136 DOI: 10.1371/journal.pcbi.1009873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 04/11/2022] [Accepted: 01/27/2022] [Indexed: 11/19/2022] Open
Abstract
Beyond natural stimuli such as growth factors and stresses, the ability to experimentally modulate at will the levels or activity of specific intracellular signaling molecule(s) in specified cells within a tissue can be a powerful tool for uncovering new regulation and tissue behaviors. Here we perturb the levels of cAMP within specific cells of an epithelial monolayer to probe the time-dynamic behavior of cell-cell communication protocols implemented by the cAMP/PKA pathway and its coupling to the ERK pathway. The time-dependent ERK responses we observe in the perturbed cells for spatially uniform cAMP perturbations (all cells) can be very different from those due to spatially localized perturbations (a few cells). Through a combination of pharmacological and genetic perturbations, signal analysis, and computational modeling, we infer how intracellular regulation and regulated cell-cell coupling each impact the intracellular ERK response in single cells. Our approach reveals how a dynamic gap junction state helps sculpt the intracellular ERK response over time in locally perturbed cells.
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Affiliation(s)
| | - Elham Aslankoohi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Andrew H. Ng
- Outpace Bio, Seattle, Washington, United States of America
| | - Michael Chevalier
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Fonseca JP, Bonny AR, Kumar GR, Ng AH, Town J, Wu QC, Aslankoohi E, Chen SY, Dods G, Harrigan P, Osimiri LC, Kistler AL, El-Samad H. A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells. ACS Synth Biol 2019; 8:2593-2606. [PMID: 31686495 DOI: 10.1021/acssynbio.9b00322] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ability to rapidly assemble and prototype cellular circuits is vital for biological research and its applications in biotechnology and medicine. Current methods for the assembly of mammalian DNA circuits are laborious, slow, and expensive. Here we present the Mammalian ToolKit (MTK), a Golden Gate-based cloning toolkit for fast, reproducible, and versatile assembly of large DNA vectors and their implementation in mammalian models. The MTK consists of a curated library of characterized, modular parts that can be assembled into transcriptional units and further weaved into complex circuits. We showcase the capabilities of the MTK by using it to generate single-integration landing pads, create and deliver libraries of protein variants and sgRNAs, and iterate through dCas9-based prototype circuits. As a biological proof of concept, we demonstrate how the MTK can speed the generation of noninfectious viral circuits to enable rapid testing of pharmacological inhibitors of emerging viruses that pose a major threat to human health.
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Affiliation(s)
- João Pedro Fonseca
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Alain R. Bonny
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - G. Renuka Kumar
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Andrew H. Ng
- Cell Design Initiative, University of California, San Francisco, San Francisco, California 94158, United States
| | - Jason Town
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Qiu Chang Wu
- Harvard Systems Biology Graduate Program, Cambridge, Massachusetts 02138, United States
| | - Elham Aslankoohi
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Susan Y. Chen
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Galen Dods
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Patrick Harrigan
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Lindsey C. Osimiri
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
- The UC Berkeley−UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, California 94132, United States
| | - Amy L. Kistler
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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Aslankoohi E, Herrera-Malaver B, Rezaei MN, Steensels J, Courtin CM, Verstrepen KJ. Non-Conventional Yeast Strains Increase the Aroma Complexity of Bread. PLoS One 2016; 11:e0165126. [PMID: 27776154 PMCID: PMC5077118 DOI: 10.1371/journal.pone.0165126] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/06/2016] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae is routinely used yeast in food fermentations because it combines several key traits, including fermentation efficiency and production of desirable flavors. However, the dominance of S. cerevisiae in industrial fermentations limits the diversity in the aroma profiles of the end products. Hence, there is a growing interest in non-conventional yeast strains that can help generate the diversity and complexity desired in today's diversified and consumer-driven markets. Here, we selected a set of non-conventional yeast strains to examine their potential for bread fermentation. Here, we tested ten non-conventional yeasts for bread fermentation, including two Saccharomyces species that are not currently used in bread making and 8 non-Saccharomyces strains. The results show that Torulaspora delbrueckii and Saccharomyces bayanus combine satisfactory dough fermentation with an interesting flavor profile. Sensory analysis and HS-SPME-GC-MS analysis confirmed that these strains produce aroma profiles that are very different from that produced by a commercial bakery strain. Moreover, bread produced with these yeasts was preferred by a majority of a trained sensory panel. These results demonstrate the potential of T. delbrueckii and S. bayanus as alternative yeasts for bread dough leavening, and provide a general experimental framework for the evaluation of more yeasts and bacteria.
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Affiliation(s)
- Elham Aslankoohi
- Systems Biology Laboratory, VIB Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- Systems Biology Laboratory, VIB Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Mohammad Naser Rezaei
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
| | - Jan Steensels
- Systems Biology Laboratory, VIB Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Christophe M. Courtin
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
- * E-mail: (KV); (CC)
| | - Kevin J. Verstrepen
- Systems Biology Laboratory, VIB Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
- * E-mail: (KV); (CC)
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11
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Aslankoohi E, Voordeckers K, Sun H, Sanchez-Rodriguez A, van der Zande E, Marchal K, Verstrepen KJ. Nucleosomes affect local transformation efficiency. Nucleic Acids Res 2012; 40:9506-12. [PMID: 22904077 PMCID: PMC3479212 DOI: 10.1093/nar/gks777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today's recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency.
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Affiliation(s)
- Elham Aslankoohi
- Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
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12
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Steensels J, Snoek T, Meersman E, Picca Nicolino M, Aslankoohi E, Christiaens JF, Gemayel R, Meert W, New AM, Pougach K, Saels V, van der Zande E, Voordeckers K, Verstrepen KJ. Selecting and generating superior yeasts for the brewing industry. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.cervis.2012.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Dardaei L, Shahsavani R, Ghavamzadeh A, Behmanesh M, Aslankoohi E, Alimoghaddam K, Ghaffari SH. The detection of disseminated tumor cells in bone marrow and peripheral blood of gastric cancer patients by multimarker (CEA, CK20, TFF1 and MUC2) quantitative real-time PCR. Clin Biochem 2010; 44:325-30. [PMID: 21130081 DOI: 10.1016/j.clinbiochem.2010.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 11/01/2010] [Accepted: 11/20/2010] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To investigate the suitability of multimarker detection of DTCs in PB and BM of GC patients. DESIGN AND METHOD A qRT-PCR assay was developed to estimate the number of CEA, CK20, TFF1 and MUC2 transcripts in PB and BM samples of 35 GC patients prior to the initiation of therapy. PB samples from healthy volunteers and BM from patients with hematological malignancies were used as negative controls. RESULTS In PB analysis; 22.9%, 37.1%, 31.4%, and 22.9% of GC patients and in BM analysis; 20%, 28.6%, 45.7%, and 22.9% of GC patients were positive for CEA, CK20, TFF1 and MUC2 mRNAs, respectively. Samples from the control group were negative for the expression of all the markers tested in this study. A higher positive ratio was obtained with the multimarker detection in comparison to the single marker detection. There was a significant correlation between the PB and BM samples for DTC detection. CONCLUSION Multimarker detection assay is a reliable and powerful tool for the early detection of DTCs in GC patients.
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Affiliation(s)
- L Dardaei
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
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